A7825503116519F70002E2DD /* chimerabellerophoncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerabellerophoncommand.cpp; sourceTree = "<group>"; };
A78434881162224F00100BE0 /* chimeraccodecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraccodecommand.h; sourceTree = "<group>"; };
A78434891162224F00100BE0 /* chimeraccodecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraccodecommand.cpp; sourceTree = "<group>"; };
+ A787A24F124CB46C0076EB84 /* getlineagecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlineagecommand.h; sourceTree = "<group>"; };
+ A787A250124CB46C0076EB84 /* getlineagecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlineagecommand.cpp; sourceTree = "<group>"; };
+ A787A28E124CE1470076EB84 /* removelineagecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removelineagecommand.h; sourceTree = "<group>"; };
+ A787A28F124CE1470076EB84 /* removelineagecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removelineagecommand.cpp; sourceTree = "<group>"; };
A798626D1240D91B005FC847 /* normalizesharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = normalizesharedcommand.h; sourceTree = "<group>"; };
A798626E1240D91B005FC847 /* normalizesharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = normalizesharedcommand.cpp; sourceTree = "<group>"; };
A7AE6302121C3408001DE6FC /* sharedrabundfloatvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedrabundfloatvector.h; sourceTree = "<group>"; };
A7DA205B113FECD400BF472F /* getgroupcommand.h */,
A7DA205C113FECD400BF472F /* getlabelcommand.cpp */,
A7DA205D113FECD400BF472F /* getlabelcommand.h */,
+ A787A24F124CB46C0076EB84 /* getlineagecommand.h */,
+ A787A250124CB46C0076EB84 /* getlineagecommand.cpp */,
A7DA205F113FECD400BF472F /* getlistcountcommand.h */,
A7DA205E113FECD400BF472F /* getlistcountcommand.cpp */,
A7DA2061113FECD400BF472F /* getoturepcommand.h */,
A7DA20EA113FECD400BF472F /* readotucommand.cpp */,
A7DA20F1113FECD400BF472F /* readtreecommand.h */,
A7DA20F0113FECD400BF472F /* readtreecommand.cpp */,
+ A787A28E124CE1470076EB84 /* removelineagecommand.h */,
+ A787A28F124CE1470076EB84 /* removelineagecommand.cpp */,
A7DA20F3113FECD400BF472F /* removeseqscommand.h */,
A7DA20F2113FECD400BF472F /* removeseqscommand.cpp */,
A7DA20F5113FECD400BF472F /* reversecommand.h */,
#include "metastatscommand.h"
#include "splitgroupscommand.h"
#include "clusterfragmentscommand.h"
+#include "getlineagecommand.h"
+#include "removelineagecommand.h"
/*******************************************************/
commands["metastats"] = "metastats";
commands["split.groups"] = "split.groups";
commands["cluster.fragments"] = "cluster.fragments";
+ commands["get.lineage"] = "get.lineage";
+ commands["remove.lineage"] = "remove.lineage";
commands["classify.seqs"] = "MPIEnabled";
commands["dist.seqs"] = "MPIEnabled";
commands["filter.seqs"] = "MPIEnabled";
else if(commandName == "metastats") { command = new MetaStatsCommand(optionString); }
else if(commandName == "split.groups") { command = new SplitGroupCommand(optionString); }
else if(commandName == "cluster.fragments") { command = new ClusterFragmentsCommand(optionString); }
+ else if(commandName == "get.lineage") { command = new GetLineageCommand(optionString); }
+ else if(commandName == "remove.lineage") { command = new RemoveLineageCommand(optionString); }
else { command = new NoCommand(optionString); }
return command;
string nextcommand = "";
int count = 0;
+ bool ignoreSemiColons = false;
//go through string until you reach ; or end
while (count < commandString.length()) {
- if (commandString[count] == ';') { break; }
+ //you want to ignore any ; until you reach the next '
+ if ((commandString[count] == '\'') && (!ignoreSemiColons)) { ignoreSemiColons = true; }
+ else if ((commandString[count] == '\'') && (ignoreSemiColons)) { ignoreSemiColons = false; }
+
+ if ((commandString[count] == ';') && (!ignoreSemiColons)) { break; }
else { nextcommand += commandString[count]; }
count++;
--- /dev/null
+/*
+ * getlineagecommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 9/24/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "getlineagecommand.h"
+#include "sequence.hpp"
+#include "listvector.hpp"
+
+//**********************************************************************************************************************
+
+GetLineageCommand::GetLineageCommand(string option) {
+ try {
+ abort = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"fasta","name", "group", "alignreport", "taxon", "dups", "list","taxonomy","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string,string>::iterator it;
+
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("alignreport");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["alignreport"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("fasta");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["fasta"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("list");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["list"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["name"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("group");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["group"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("taxonomy");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["taxonomy"] = inputDir + it->second; }
+ }
+ }
+
+
+ //check for required parameters
+ fastafile = validParameter.validFile(parameters, "fasta", true);
+ if (fastafile == "not open") { abort = true; }
+ else if (fastafile == "not found") { fastafile = ""; }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; }
+
+ alignfile = validParameter.validFile(parameters, "alignreport", true);
+ if (alignfile == "not open") { abort = true; }
+ else if (alignfile == "not found") { alignfile = ""; }
+
+ listfile = validParameter.validFile(parameters, "list", true);
+ if (listfile == "not open") { abort = true; }
+ else if (listfile == "not found") { listfile = ""; }
+
+ taxfile = validParameter.validFile(parameters, "taxonomy", true);
+ if (taxfile == "not open") { abort = true; }
+ else if (taxfile == "not found") { taxfile = ""; m->mothurOut("The taxonomy parameter is required for the get.lineage command."); m->mothurOutEndLine(); abort = true; }
+
+ string usedDups = "true";
+ string temp = validParameter.validFile(parameters, "dups", false); if (temp == "not found") { temp = "false"; usedDups = ""; }
+ dups = m->isTrue(temp);
+
+ taxons = validParameter.validFile(parameters, "taxon", false);
+ if (taxons == "not found") { taxons = ""; m->mothurOut("No taxons given, please correct."); m->mothurOutEndLine(); abort = true; }
+ else {
+ //rip off quotes
+ if (taxons[0] == '\'') { taxons = taxons.substr(1); }
+ if (taxons[(taxons.length()-1)] == '\'') { taxons = taxons.substr(0, (taxons.length()-1)); }
+ }
+
+
+ if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "")) { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport, taxonomy or listfile."); m->mothurOutEndLine(); abort = true; }
+
+ if ((usedDups != "") && (namefile == "")) { m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine(); abort = true; }
+
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "GetLineageCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+void GetLineageCommand::help(){
+ try {
+ m->mothurOut("The get.lineage command reads a taxonomy file and any of the following file types: fasta, name, group, list or alignreport file.\n");
+ m->mothurOut("It outputs a file containing only the sequences from the taxonomy file that are from the taxon requested.\n");
+ m->mothurOut("The get.lineage command parameters are taxon, fasta, name, group, list, taxonomy, alignreport and dups. You must provide taxonomy and taxon.\n");
+ m->mothurOut("The dups parameter allows you to add the entire line from a name file if you add any name from the line. default=false. \n");
+ m->mothurOut("The taxon parameter allows you to select the taxons you would like to get.\n");
+ m->mothurOut("The get.lineage command should be in the following format: get.lineage(taxonomy=yourTaxonomyFile, taxon=yourTaxons).\n");
+ m->mothurOut("Example get.lineage(taxonomy=amazon.silva.taxonomy, taxon=Bacteria;Firmicutes;Bacilli;Lactobacillales;).\n");
+ m->mothurOut("Note: If you are running mothur in script mode you must wrap the taxon in ' characters so mothur will ignore the ; in the taxon.\n");
+ m->mothurOut("Example get.lineage(taxonomy=amazon.silva.taxonomy, taxon='Bacteria;Firmicutes;Bacilli;Lactobacillales;').\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "help");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+int GetLineageCommand::execute(){
+ try {
+
+ if (abort == true) { return 0; }
+
+ if (m->control_pressed) { return 0; }
+
+ //read through the correct file and output lines you want to keep
+ if (taxfile != "") { readTax(); } //fills the set of names to get
+ if (namefile != "") { readName(); }
+ if (fastafile != "") { readFasta(); }
+ if (groupfile != "") { readGroup(); }
+ if (alignfile != "") { readAlign(); }
+ if (listfile != "") { readList(); }
+
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ if (outputNames.size() != 0) {
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+ }
+
+ return 0;
+ }
+
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "execute");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int GetLineageCommand::readFasta(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+
+ ifstream in;
+ m->openInputFile(fastafile, in);
+ string name;
+
+ bool wroteSomething = false;
+
+ while(!in.eof()){
+
+ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+
+ Sequence currSeq(in);
+ name = currSeq.getName();
+
+ if (name != "") {
+ //if this name is in the accnos file
+ if (names.count(name) != 0) {
+ wroteSomething = true;
+
+ currSeq.printSequence(out);
+ }
+ }
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName);
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "readFasta");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int GetLineageCommand::readList(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" + m->getExtension(listfile);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(listfile, in);
+
+ bool wroteSomething = false;
+
+ while(!in.eof()){
+
+ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+
+ //read in list vector
+ ListVector list(in);
+
+ //make a new list vector
+ ListVector newList;
+ newList.setLabel(list.getLabel());
+
+ //for each bin
+ for (int i = 0; i < list.getNumBins(); i++) {
+
+ //parse out names that are in accnos file
+ string binnames = list.get(i);
+
+ string newNames = "";
+ while (binnames.find_first_of(',') != -1) {
+ string name = binnames.substr(0,binnames.find_first_of(','));
+ binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
+
+ //if that name is in the .accnos file, add it
+ if (names.count(name) != 0) { newNames += name + ","; }
+ }
+
+ //get last name
+ if (names.count(binnames) != 0) { newNames += binnames + ","; }
+
+ //if there are names in this bin add to new list
+ if (newNames != "") {
+ newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
+ newList.push_back(newNames);
+ }
+ }
+
+ //print new listvector
+ if (newList.getNumBins() != 0) {
+ wroteSomething = true;
+ newList.print(out);
+ }
+
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName);
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "readList");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int GetLineageCommand::readName(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+
+ ifstream in;
+ m->openInputFile(namefile, in);
+ string name, firstCol, secondCol;
+
+ bool wroteSomething = false;
+
+
+ while(!in.eof()){
+
+ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+
+ in >> firstCol;
+ in >> secondCol;
+
+ string hold = "";
+ if (dups) { hold = secondCol; }
+
+ vector<string> parsedNames;
+ //parse second column saving each name
+ while (secondCol.find_first_of(',') != -1) {
+ name = secondCol.substr(0,secondCol.find_first_of(','));
+ secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
+ parsedNames.push_back(name);
+ }
+
+ //get name after last ,
+ parsedNames.push_back(secondCol);
+
+ vector<string> validSecond;
+ for (int i = 0; i < parsedNames.size(); i++) {
+ if (names.count(parsedNames[i]) != 0) {
+ validSecond.push_back(parsedNames[i]);
+ }
+ }
+
+ if ((dups) && (validSecond.size() != 0)) { //dups = true and we want to add someone, then add everyone
+ for (int i = 0; i < parsedNames.size(); i++) { names.insert(parsedNames[i]); }
+ out << firstCol << '\t' << hold << endl;
+ wroteSomething = true;
+ }else {
+ //if the name in the first column is in the set then print it and any other names in second column also in set
+ if (names.count(firstCol) != 0) {
+
+ wroteSomething = true;
+
+ out << firstCol << '\t';
+
+ //you know you have at least one valid second since first column is valid
+ for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
+ out << validSecond[validSecond.size()-1] << endl;
+
+
+ //make first name in set you come to first column and then add the remaining names to second column
+ }else {
+ //you want part of this row
+ if (validSecond.size() != 0) {
+
+ wroteSomething = true;
+
+ out << validSecond[0] << '\t';
+
+ //you know you have at least one valid second since first column is valid
+ for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
+ out << validSecond[validSecond.size()-1] << endl;
+ }
+ }
+ }
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName);
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "readName");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int GetLineageCommand::readGroup(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+
+ ifstream in;
+ m->openInputFile(groupfile, in);
+ string name, group;
+
+ bool wroteSomething = false;
+
+ while(!in.eof()){
+
+ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+
+
+ in >> name; //read from first column
+ in >> group; //read from second column
+
+ //if this name is in the accnos file
+ if (names.count(name) != 0) {
+ wroteSomething = true;
+
+ out << name << '\t' << group << endl;
+ }
+
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName);
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "readGroup");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int GetLineageCommand::readTax(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(taxfile, in);
+ string name, tax;
+
+ bool wroteSomething = false;
+
+ while(!in.eof()){
+
+ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+
+ in >> name; //read from first column
+ in >> tax; //read from second column
+
+ string newtax = tax;
+
+ //if the users file contains confidence scores we want to ignore them when searching for the taxons
+ int hasConfidences = tax.find_first_of('(');
+ if (hasConfidences != string::npos) {
+ newtax = removeConfidences(tax);
+ }
+
+ int pos = newtax.find(taxons);
+
+ if (pos != string::npos) { //this sequence contains the taxon the user wants
+ names.insert(name);
+ out << name << '\t' << tax << endl;
+ }
+
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (names.size() == 0) { m->mothurOut("Your taxonomy file does not contain any sequences from " + taxons + "."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName);
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "readTax");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+string GetLineageCommand::removeConfidences(string tax) {
+ try {
+
+ string taxon = "";
+ int taxLength = tax.length();
+ for(int i=0;i<taxLength;i++){
+ if(tax[i] == ';'){
+ taxon = taxon.substr(0, taxon.find_first_of('(')); //rip off confidence
+ taxon += ";";
+ }
+ else{
+ taxon += tax[i];
+ }
+ }
+
+ return taxon;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "removeConfidences");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//alignreport file has a column header line then all other lines contain 16 columns. we just want the first column since that contains the name
+int GetLineageCommand::readAlign(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(alignfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report";
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+
+ ifstream in;
+ m->openInputFile(alignfile, in);
+ string name, junk;
+
+ bool wroteSomething = false;
+
+ //read column headers
+ for (int i = 0; i < 16; i++) {
+ if (!in.eof()) { in >> junk; out << junk << '\t'; }
+ else { break; }
+ }
+ out << endl;
+
+ while(!in.eof()){
+
+ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+
+
+ in >> name; //read from first column
+
+ //if this name is in the accnos file
+ if (names.count(name) != 0) {
+ wroteSomething = true;
+
+ out << name << '\t';
+
+ //read rest
+ for (int i = 0; i < 15; i++) {
+ if (!in.eof()) { in >> junk; out << junk << '\t'; }
+ else { break; }
+ }
+ out << endl;
+
+ }else {//still read just don't do anything with it
+ //read rest
+ for (int i = 0; i < 15; i++) {
+ if (!in.eof()) { in >> junk; }
+ else { break; }
+ }
+ }
+
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName);
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "readAlign");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+
+
+
--- /dev/null
+#ifndef GETLINEAGECOMMAND_H
+#define GETLINEAGECOMMAND_H
+
+/*
+ * getlineagecommand.h
+ * Mothur
+ *
+ * Created by westcott on 9/24/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+
+class GetLineageCommand : public Command {
+
+ public:
+
+ GetLineageCommand(string);
+ ~GetLineageCommand(){};
+ int execute();
+ void help();
+
+ private:
+ set<string> names;
+ vector<string> outputNames;
+ string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
+ bool abort, dups;
+
+ int readFasta();
+ int readName();
+ int readGroup();
+ int readAlign();
+ int readList();
+ int readTax();
+ string removeConfidences(string);
+};
+
+#endif
+
--- /dev/null
+/*
+ * removelineagecommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 9/24/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "removelineagecommand.h"
+#include "sequence.hpp"
+#include "listvector.hpp"
+
+//**********************************************************************************************************************
+
+RemoveLineageCommand::RemoveLineageCommand(string option) {
+ try {
+ abort = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"fasta","name", "group", "alignreport", "taxon", "dups", "list","taxonomy","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string,string>::iterator it;
+
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("alignreport");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["alignreport"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("fasta");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["fasta"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("list");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["list"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["name"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("group");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["group"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("taxonomy");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["taxonomy"] = inputDir + it->second; }
+ }
+ }
+
+
+ //check for required parameters
+ fastafile = validParameter.validFile(parameters, "fasta", true);
+ if (fastafile == "not open") { abort = true; }
+ else if (fastafile == "not found") { fastafile = ""; }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; }
+
+ alignfile = validParameter.validFile(parameters, "alignreport", true);
+ if (alignfile == "not open") { abort = true; }
+ else if (alignfile == "not found") { alignfile = ""; }
+
+ listfile = validParameter.validFile(parameters, "list", true);
+ if (listfile == "not open") { abort = true; }
+ else if (listfile == "not found") { listfile = ""; }
+
+ taxfile = validParameter.validFile(parameters, "taxonomy", true);
+ if (taxfile == "not open") { abort = true; }
+ else if (taxfile == "not found") { taxfile = ""; m->mothurOut("The taxonomy parameter is required for the get.lineage command."); m->mothurOutEndLine(); abort = true; }
+
+ string usedDups = "true";
+ string temp = validParameter.validFile(parameters, "dups", false); if (temp == "not found") { temp = "false"; usedDups = ""; }
+ dups = m->isTrue(temp);
+
+ taxons = validParameter.validFile(parameters, "taxon", false);
+ if (taxons == "not found") { taxons = ""; m->mothurOut("No taxons given, please correct."); m->mothurOutEndLine(); abort = true; }
+ else {
+ //rip off quotes
+ if (taxons[0] == '\'') { taxons = taxons.substr(1); }
+ if (taxons[(taxons.length()-1)] == '\'') { taxons = taxons.substr(0, (taxons.length()-1)); }
+ }
+
+
+ if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "")) { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport, taxonomy or listfile."); m->mothurOutEndLine(); abort = true; }
+
+ if ((usedDups != "") && (namefile == "")) { m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine(); abort = true; }
+
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveLineageCommand", "RemoveLineageCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+void RemoveLineageCommand::help(){
+ try {
+ m->mothurOut("The remove.lineage command reads a taxonomy file and any of the following file types: fasta, name, group, list or alignreport file.\n");
+ m->mothurOut("It outputs a file containing only the sequences from the taxonomy file that are not from the taxon you requested to be removed.\n");
+ m->mothurOut("The remove.lineage command parameters are taxon, fasta, name, group, list, taxonomy, alignreport and dups. You must provide taxonomy and taxon.\n");
+ m->mothurOut("The dups parameter allows you to add the entire line from a name file if you add any name from the line. default=false. \n");
+ m->mothurOut("The taxon parameter allows you to select the taxons you would like to remove.\n");
+ m->mothurOut("The remove.lineage command should be in the following format: remove.lineage(taxonomy=yourTaxonomyFile, taxon=yourTaxons).\n");
+ m->mothurOut("Example remove.lineage(taxonomy=amazon.silva.taxonomy, taxon=Bacteria;Firmicutes;Bacilli;Lactobacillales;).\n");
+ m->mothurOut("Note: If you are running mothur in script mode you must wrap the taxon in ' characters so mothur will ignore the ; in the taxon.\n");
+ m->mothurOut("Example remove.lineage(taxonomy=amazon.silva.taxonomy, taxon='Bacteria;Firmicutes;Bacilli;Lactobacillales;').\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveLineageCommand", "help");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+int RemoveLineageCommand::execute(){
+ try {
+
+ if (abort == true) { return 0; }
+
+ if (m->control_pressed) { return 0; }
+
+ //read through the correct file and output lines you want to keep
+ if (taxfile != "") { readTax(); } //fills the set of names to remove
+ if (namefile != "") { readName(); }
+ if (fastafile != "") { readFasta(); }
+ if (groupfile != "") { readGroup(); }
+ if (alignfile != "") { readAlign(); }
+ if (listfile != "") { readList(); }
+
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ if (outputNames.size() != 0) {
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+ }
+
+ return 0;
+ }
+
+ catch(exception& e) {
+ m->errorOut(e, "RemoveLineageCommand", "execute");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int RemoveLineageCommand::readFasta(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(fastafile, in);
+ string name;
+
+ bool wroteSomething = false;
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+
+ Sequence currSeq(in);
+ name = currSeq.getName();
+
+ if (name != "") {
+ //if this name is in the accnos file
+ if (names.count(name) == 0) {
+ wroteSomething = true;
+
+ currSeq.printSequence(out);
+ }
+ }
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your fasta file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName);
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveLineageCommand", "readFasta");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int RemoveLineageCommand::readList(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" + m->getExtension(listfile);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(listfile, in);
+
+ bool wroteSomething = false;
+
+ while(!in.eof()){
+ //read in list vector
+ ListVector list(in);
+
+ //make a new list vector
+ ListVector newList;
+ newList.setLabel(list.getLabel());
+
+ //for each bin
+ for (int i = 0; i < list.getNumBins(); i++) {
+ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+
+ //parse out names that are in accnos file
+ string binnames = list.get(i);
+
+ string newNames = "";
+ while (binnames.find_first_of(',') != -1) {
+ string name = binnames.substr(0,binnames.find_first_of(','));
+ binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
+
+ //if that name is in the .accnos file, add it
+ if (names.count(name) == 0) { newNames += name + ","; }
+ }
+
+ //get last name
+ if (names.count(binnames) == 0) { newNames += binnames + ","; }
+
+ //if there are names in this bin add to new list
+ if (newNames != "") {
+ newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
+ newList.push_back(newNames);
+ }
+ }
+
+ //print new listvector
+ if (newList.getNumBins() != 0) {
+ wroteSomething = true;
+ newList.print(out);
+ }
+
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your list file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName);
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveLineageCommand", "readList");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int RemoveLineageCommand::readName(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(namefile, in);
+ string name, firstCol, secondCol;
+
+ bool wroteSomething = false;
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+
+ in >> firstCol;
+ in >> secondCol;
+
+ vector<string> parsedNames;
+ //parse second column saving each name
+ while (secondCol.find_first_of(',') != -1) {
+ name = secondCol.substr(0,secondCol.find_first_of(','));
+ secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
+ parsedNames.push_back(name);
+ }
+
+ //get name after last ,
+ parsedNames.push_back(secondCol);
+
+ vector<string> validSecond; validSecond.clear();
+ for (int i = 0; i < parsedNames.size(); i++) {
+ if (names.count(parsedNames[i]) == 0) {
+ validSecond.push_back(parsedNames[i]);
+ }
+ }
+
+ if ((dups) && (validSecond.size() != parsedNames.size())) { //if dups is true and we want to get rid of anyone, get rid of everyone
+ for (int i = 0; i < parsedNames.size(); i++) { names.insert(parsedNames[i]); }
+ }else {
+ //if the name in the first column is in the set then print it and any other names in second column also in set
+ if (names.count(firstCol) == 0) {
+
+ wroteSomething = true;
+
+ out << firstCol << '\t';
+
+ //you know you have at least one valid second since first column is valid
+ for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
+ out << validSecond[validSecond.size()-1] << endl;
+
+ //make first name in set you come to first column and then add the remaining names to second column
+ }else {
+
+ //you want part of this row
+ if (validSecond.size() != 0) {
+
+ wroteSomething = true;
+
+ out << validSecond[0] << '\t';
+
+ //you know you have at least one valid second since first column is valid
+ for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
+ out << validSecond[validSecond.size()-1] << endl;
+ }
+ }
+ }
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your name file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName);
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveLineageCommand", "readName");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int RemoveLineageCommand::readGroup(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(groupfile, in);
+ string name, group;
+
+ bool wroteSomething = false;
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+
+ in >> name; //read from first column
+ in >> group; //read from second column
+
+ //if this name is in the accnos file
+ if (names.count(name) == 0) {
+ wroteSomething = true;
+ out << name << '\t' << group << endl;
+ }
+
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your group file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName);
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveLineageCommand", "readGroup");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int RemoveLineageCommand::readTax(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(taxfile, in);
+ string name, tax;
+
+ bool wroteSomething = false;
+
+ while(!in.eof()){
+
+ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+
+ in >> name; //read from first column
+ in >> tax; //read from second column
+
+ string newtax = tax;
+
+ //if the users file contains confidence scores we want to ignore them when searching for the taxons
+ int hasConfidences = tax.find_first_of('(');
+ if (hasConfidences != string::npos) {
+ newtax = removeConfidences(tax);
+ }
+
+ int pos = newtax.find(taxons);
+
+ if (pos == string::npos) {
+ wroteSomething = true;
+ out << name << '\t' << tax << endl;
+ }else{ //this sequence contains the taxon the user wants to remove
+ names.insert(name);
+ }
+
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (!wroteSomething) { m->mothurOut("Your taxonomy file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName);
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveLineageCommand", "readTax");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+string RemoveLineageCommand::removeConfidences(string tax) {
+ try {
+
+ string taxon = "";
+ int taxLength = tax.length();
+ for(int i=0;i<taxLength;i++){
+ if(tax[i] == ';'){
+ taxon = taxon.substr(0, taxon.find_first_of('(')); //rip off confidence
+ taxon += ";";
+ }
+ else{
+ taxon += tax[i];
+ }
+ }
+
+ return taxon;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveLineageCommand", "removeConfidences");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//alignreport file has a column header line then all other lines contain 16 columns. we just want the first column since that contains the name
+int RemoveLineageCommand::readAlign(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(alignfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report";
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(alignfile, in);
+ string name, junk;
+
+ bool wroteSomething = false;
+
+ //read column headers
+ for (int i = 0; i < 16; i++) {
+ if (!in.eof()) { in >> junk; out << junk << '\t'; }
+ else { break; }
+ }
+ out << endl;
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+
+ in >> name; //read from first column
+
+ //if this name is in the accnos file
+ if (names.count(name) == 0) {
+ wroteSomething = true;
+
+ out << name << '\t';
+
+ //read rest
+ for (int i = 0; i < 15; i++) {
+ if (!in.eof()) { in >> junk; out << junk << '\t'; }
+ else { break; }
+ }
+ out << endl;
+
+ }else {//still read just don't do anything with it
+
+ //read rest
+ for (int i = 0; i < 15; i++) {
+ if (!in.eof()) { in >> junk; }
+ else { break; }
+ }
+ }
+
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your align file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName);
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveLineageCommand", "readAlign");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
--- /dev/null
+#ifndef REMOVELINEAGECOMMAND_H
+#define REMOVELINEAGECOMMAND_H
+
+/*
+ * removelineagecommand.h
+ * Mothur
+ *
+ * Created by westcott on 9/24/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+
+class RemoveLineageCommand : public Command {
+
+ public:
+
+ RemoveLineageCommand(string);
+ ~RemoveLineageCommand(){};
+ int execute();
+ void help();
+
+ private:
+ set<string> names;
+ vector<string> outputNames;
+ string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
+ bool abort, dups;
+
+ int readFasta();
+ int readName();
+ int readGroup();
+ int readAlign();
+ int readList();
+ int readTax();
+ string removeConfidences(string);
+};
+
+#endif
+
projects / mothur.git / commitdiff